--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inputs/no_fa_ext/ApApomp_trinity	Sun Dec 03 04:30:59 2017 -0500
@@ -0,0 +1,135 @@
+>Gene.41::Ap101_1/1_1.000_309::g.41::m.41 Gene.41::Ap101_1/1_1.000_309::g.41  ORF type:internal len:104 (+) Ap101_1/1_1.000_309:1-309(+)
+VCVCVCARCVCVCATCKLCTWCVPKEKLLKHNGPPIDHNDPTTKQNLGHFISRTIWKLNS
+SLSNCNHSPRTHNHSSPSSPGEFKFTVNNEDKGIFVCQIKVEQ
+>Gene.42::Ap102_1/1_1.000_382::g.42::m.42 Gene.42::Ap102_1/1_1.000_382::g.42  ORF type:internal len:128 (+) Ap102_1/1_1.000_382:1-381(+)
+TDEYDPQRPNDYESYIKMRKDQRQREREEERKRELEEREKRRRERHRDEYDSDEDDEFNR
+KRRRSRRDDDDDHRRSSEHKARGAAIAPPQSLIESSKPDPKEVSLPQPENKLTLNTGEYG
+GGFSVGK
+>Gene.43::Ap108_1/1_1.000_314::g.43::m.43 Gene.43::Ap108_1/1_1.000_314::g.43  ORF type:internal len:105 (+) Ap108_1/1_1.000_314:1-312(+)
+LDDMDIFNSPPLGIFSVIRKMPDAAELEKTMSLYDRIQRDLELAEMTYPPQNAFEEWSRW
+TKEGKMWIYPVDNEQGMEEEANVGFHEHVFLDHMLEDFPKRGPV
+>Gene.7::Ap10_1/1_1.000_338::g.7::m.7 Gene.7::Ap10_1/1_1.000_338::g.7  ORF type:internal len:113 (+) Ap10_1/1_1.000_338:1-336(+)
+PYSAAKTTAQAATDDLKRRQEELERKAEELQRKEQELQRNMGHQARVNNFPPLPEKCCVQ
+PCFYQDFELDIPLEFQRIVKTVYYVWIAYICLLILNVLGTLAYFIAASKAGH
+>Gene.8::Ap11_1/1_1.000_406::g.8::m.8 Gene.8::Ap11_1/1_1.000_406::g.8  ORF type:internal len:136 (+) Ap11_1/1_1.000_406:1-405(+)
+EVPSVAVPGVVSTVVQDSAHKIFIGGLPNYLNEDQVKELLTSFGPLKAFNLVKDSATGLS
+KGYAFCEYLDPSITDQACAGLNGMQLGDKKLIVQRASVGAKNAQGGPNVLPVQLQIPGLN
+MAQVQGPGPTTEVLC
+>Gene.9::Ap12_1/1_1.000_582::g.9::m.9 Gene.9::Ap12_1/1_1.000_582::g.9  ORF type:internal len:195 (+) Ap12_1/1_1.000_582:1-582(+)
+DGVALFCFLHAFYLVKTQPLLLSLFMFVVVLFCYFLSSRPDTMLSHKHEVIGRFPSMSTY
+IYFSPLLVHPSIHSSTCLSSTPFWLLLASAVAVVIVGGGGDVSSVGVDGHSSQRHLSASG
+GVGLFRCRSTSCAERHLATRMRYDVARPPLKSPVIGPHTHTHSCNNKTDKTLALLRIQSL
+FNRLALVHVTIWGR
+>Gene.11::Ap13_1/1_1.000_481::g.11::m.11 Gene.11::Ap13_1/1_1.000_481::g.11  ORF type:internal len:161 (+) Ap13_1/1_1.000_481:1-480(+)
+VESRAVKKMSLVDAIRNGLYDQEHGTISDPNTATDMTVLEAINKGLIDTKNIRVNVPGTS
+EIISIDSALAENILDPLSGVLSNPATGECVDLLEAEQAGLMFVGVSEEQLKQPDLKQIVT
+EGLCDPDSGTIQDPDTGKNMTVIEAMQTGLVDSTAPLLTV
+>Gene.13::Ap18_1/1_1.000_318::g.13::m.13 Gene.13::Ap18_1/1_1.000_318::g.13  ORF type:internal len:107 (+) Ap18_1/1_1.000_318:1-318(+)
+PACKTPFYFVCQSRSKVTTVVSEKHTDAELVHTLCIRHRSTVAWDILAGERAKFSQPRAE
+SVSSASDWRVFGSDRRSIGRVPSIDLCPFSASRRICLHSGRRPSQP
+>Gene.14::Ap19_1/1_1.000_302::g.14::m.14 Gene.14::Ap19_1/1_1.000_302::g.14  ORF type:internal len:101 (+) Ap19_1/1_1.000_302:1-300(+)
+PAIVQRASGLAMSEIYHLRFCDGDRLNVSCPDNWQIHISSSYFVYVSGVDGRGVRDCRQQ
+FNGTSQCLRKIQFYDPTYFGQLIQSCQSKQRCDDGLLAKT
+>Gene.15::Ap20_1/1_1.000_780::g.15::m.15 Gene.15::Ap20_1/1_1.000_780::g.15  ORF type:internal len:261 (+) Ap20_1/1_1.000_780:1-780(+)
+HEGPVWQVAWAHPMFGNLIASCSYDRKVIIWKETGGTWAKLYEYNNHDSSVNSVCWAPYE
+FGLMLACGSSDGSVSVISSTGDGTWDSKKINNAHRIGCNAVSWGPAVQHGALLDPSGSQK
+PVKRFVTGGCDNLVKIWKEENDQWIEEQKLDGHCDWVRDVAWAPSIGLPRTVIASCSQDC
+QVIIWTNDGSGNWTSKVLHKFNAAVWHVSWSVTGNILAVSGGDNKVSLWKETIEGQWVCV
+SDVNKGHGQGQITENKSVVS
+>Gene.16::Ap21_1/1_1.000_468::g.16::m.16 Gene.16::Ap21_1/1_1.000_468::g.16  ORF type:internal len:157 (+) Ap21_1/1_1.000_468:1-468(+)
+AAIQNAKYIIAQVNPNMPRTFGDGVIHMSHCDAMVQVTDPLPEIHVSKCTEVETKIGKFI
+ADNLVHDGATLQMGIGSIPDAVLAQLGEHRDIGIHTEMFSDGVIDLVMKGVITNSKKVIQ
+TGKILSSFAFGTKKLYNFMNNNPFVVMCDVAFVNNT
+>Gene.18::Ap23_1/1_1.000_307::g.18::m.18 Gene.18::Ap23_1/1_1.000_307::g.18  ORF type:internal len:103 (-) Ap23_1/1_1.000_307:1-306(-)
+CVTTIPVITEAVYCVSIKWVPRIIVPGWLTVSMSLYCRKFLSDTCVVSQCHQTFPDVLLI
+TSSFLDNLDAEIFSSSFASVRTRPPSLKTNVYFFSTTWLVTL
+>Gene.19::Ap32_1/1_1.000_302::g.19::m.19 Gene.19::Ap32_1/1_1.000_302::g.19  ORF type:internal len:101 (+) Ap32_1/1_1.000_302:1-300(+)
+FLEEIKIAACDKEKRLSDLGEKVRQLEAQLAQQIKECEMKDFSLQQEMAKCAELTAAIQG
+KEATISELSTGLTEKTNQMMMMLNENQQKAEHIEALQTET
+>Gene.20::Ap33_1/1_1.000_569::g.20::m.20 Gene.20::Ap33_1/1_1.000_569::g.20  ORF type:internal len:190 (+) Ap33_1/1_1.000_569:1-567(+)
+CNSDAPGNIGNHCFHSNVIGTTSHDNITPHQVQNYQYQSPSMTSSMTSSSSLVSSMNNSS
+MGSPQVYANQMDSANANSPMSRSYDGGLTYAQYKNQLRPKGGFYSQYSGDHPSSTSSSTE
+SLNSKCSVSSNNTSQPSEVTRRPISTSKGHVAQAINRFSQPVTQASNTNNVNRVETGTSS
+TGSVSIMPS
+>Gene.21::Ap34_1/1_1.000_337::g.21::m.21 Gene.21::Ap34_1/1_1.000_337::g.21  ORF type:internal len:113 (+) Ap34_1/1_1.000_337:1-336(+)
+KQLTVCTEGQFKCANHHCISASSVCDKYDDCGDMSDEIGCHKDSSEGCSVNNGGCEQNCT
+DLPDKGHVCHCDPGYIVNQDDKTSCSDVDECASWGNKCSQICHNIKGSYKCA
+>Gene.22::Ap35_1/1_1.000_319::g.22::m.22 Gene.22::Ap35_1/1_1.000_319::g.22  ORF type:internal len:107 (+) Ap35_1/1_1.000_319:1-318(+)
+AEAMMDKIETFNVPRDLSEILAQSYENVKMIVMTQHEVKSERFESKVILLTDCRLIITST
+KIPCKEEQSFNLLGIRSLESKTSSRLNFSADGKQWSFMISDTDRID
+>Gene.23::Ap36_1/1_1.000_303::g.23::m.23 Gene.23::Ap36_1/1_1.000_303::g.23  ORF type:internal len:102 (+) Ap36_1/1_1.000_303:1-303(+)
+GKGIRTVAPPPGVGSARVRRDSALSDEEDVFHEDSKPTSPPAAHSPPKPKEEKILVPAPP
+PKENIWEKRKTGSSPSGSGTSQPSETSTELDEHHEPSNEYS
+>Gene.1::Ap3_1/1_1.000_546::g.1::m.1 Gene.1::Ap3_1/1_1.000_546::g.1  ORF type:internal len:183 (+) Ap3_1/1_1.000_546:1-546(+)
+AMQYTGLLLFCLFALTAAKPAEDLQMLIRALLHEIEEEGELQERGIGAVKYGGTNVGEDY
+VEVKVIRNMEEVKADQKSHKPLYSLIYGKGTHDPNSSQHSLTSWTWSQLDKCQNGAEGCF
+MIRNLKPNTEYWFQLEVQMWINGAYEYIESRKDVEQIRTKGRQENAPWMSSKSYKPDADI
+RT
+>Gene.25::Ap43_1/1_1.000_684::g.25::m.25 Gene.25::Ap43_1/1_1.000_684::g.25  ORF type:internal len:229 (+) Ap43_1/1_1.000_684:1-684(+)
+PSEVTKLQKTEMTAAQSKKLASGPMEDVGCEHDDSLPKIADGQVGKESVEQGISIMEYDT
+EPGSKISHGVPERGRTHTRTSAGNVVESKLELEFNQSLTDMEVAQITDAAEARRKAREAA
+RAQRLWHKKMIEEGKDPRVMLKSRSHSSPSPDTYTIVVEGSAEVNTSKDKVVSISPTQVQ
+GEEGQFAFHDSKKDIKKKTKKSTESLNEEVEKKKKKKKTISANETGSQ
+>Gene.26::Ap48_1/1_1.000_347::g.26::m.26 Gene.26::Ap48_1/1_1.000_347::g.26  ORF type:internal len:116 (+) Ap48_1/1_1.000_347:1-345(+)
+YWWLMPTMLYGLLWWRGSQAGYTFSEILCVYGYSLAIYIPISILWVIQISWLQWMLVMIG
+MALSGTVLVLTFWPAVSQDDRKISMITMVMIVLFHGLLAIGFVLYFFHVPSHVPT
+>Gene.27::Ap50_1/1_1.000_299::g.27::m.27 Gene.27::Ap50_1/1_1.000_299::g.27  ORF type:internal len:100 (+) Ap50_1/1_1.000_299:1-297(+)
+EIVYRNYIDISVAVATPKGLVVPVLRDVGNMNYAEIEKGLNELGEKARTGNLAIEDMDGG
+TFTISNGGVFGSLLGTPIINPPQSAILGMHGIFDRPVAI
+>Gene.28::Ap51_1/1_1.000_363::g.28::m.28 Gene.28::Ap51_1/1_1.000_363::g.28  ORF type:internal len:122 (+) Ap51_1/1_1.000_363:1-363(+)
+DKDKFKDLYRWTYKFGLDSEAGQRTLPVDMAISLWQLVFSERQPPILKQWLNFLNVHRNV
+RGIPRDTWDMFLNFVEAVGDDLSSYDDTEAWPSLFDDFVEYENDRQNQNVKVDKVERDYY
+D
+>Gene.29::Ap59_1/1_1.000_402::g.29::m.29 Gene.29::Ap59_1/1_1.000_402::g.29  ORF type:internal len:135 (+) Ap59_1/1_1.000_402:1-402(+)
+PRMINIQSTGWLLHRLHEGANINTAGVKDTPIALFCAGSSQHNLHRVLCLFSGCVCRTCS
+DHICCVLLMNPEKELVGFGIQNSLALHLCRLTNASLCACVSMHMYFVCICITSVHMYLIY
+KAFNLYMLNQQKQI
+>Gene.30::Ap67_1/1_1.000_300::g.30::m.30 Gene.30::Ap67_1/1_1.000_300::g.30  ORF type:internal len:101 (+) Ap67_1/1_1.000_300:1-300(+)
+RHWTVLGLRLQGDFFGLPRSGKMSEAVNPESTSSILPTITLSTDTDQAWPQLIWIPYVTL
+TLILLLLTCLSFMHYHFKNRGKYLDAVYKQNNLTPCPKKY
+>Gene.31::Ap68_1/1_1.000_323::g.31::m.31 Gene.31::Ap68_1/1_1.000_323::g.31  ORF type:internal len:108 (+) Ap68_1/1_1.000_323:1-321(+)
+GRTRDHQQLLEASKCKPIQYPKPDGVVSFDLLSSVALTGTNHDHDQPPHLTLKDDEVPVA
+RNLAIYDGPEERFCPAGVYEFIDTDQGKRLQINAQNCIHCKTCDIKC
+>Gene.2::Ap6_1/1_1.000_390::g.2::m.2 Gene.2::Ap6_1/1_1.000_390::g.2  ORF type:internal len:131 (+) Ap6_1/1_1.000_390:1-390(+)
+ENVLASHCPVGLSSTRYWQSEMADLPPGDAERGKKIFIQRCAHCHSVEAGGKHKQGPNLH
+GFIGRKTGQAPGYTFTEANLKKGIIWDKETLDIYLENPKKYIPGTKMIFPGLKKKADRAD
+LIAYLEESTK
+>Gene.32::Ap75_1/1_1.000_532::g.32::m.32 Gene.32::Ap75_1/1_1.000_532::g.32  ORF type:internal len:178 (+) Ap75_1/1_1.000_532:1-531(+)
+LEAAKKEITSQKERMSEMKGHLSAMAAITSGPEPDDVEVATSDEDFDDTHPELAAMKKSM
+HQQEMRYSAALNQICDLQEQVKILQEKLAETQDKESEAQLREEVTKLRNKVMEYEETMKT
+LEEDLKTMSQIAGESQGSLNTTQDELIKVTEDLAQLYHLICELNGETPNRVMLEHVQ
+>Gene.33::Ap77_1/1_1.000_337::g.33::m.33 Gene.33::Ap77_1/1_1.000_337::g.33  ORF type:internal len:113 (+) Ap77_1/1_1.000_337:1-336(+)
+CMAPPHSPMQYTWPFGHLYQCPLDRPIAVSICFLSSSLIPNPVRNTNRCSSFRASSTSFL
+STSVSGVFLFNNCLAFSNFSSTTAFIFGFVSWILMSYSIVFARRRRRIFSIS
+>Gene.35::Ap78_1/1_1.000_428::g.35::m.35 Gene.35::Ap78_1/1_1.000_428::g.35  ORF type:internal len:143 (+) Ap78_1/1_1.000_428:1-426(+)
+VSRSEERRSTLGIITVKTIREPLRPYVIKRVLDPRTGEWISEQQASKEEILFVSRGIYHN
+RKTGERMLIAEAIEKKLVEAEYLGDAPEPEVISNTYAVRSVVDLRLKKVITFGEAVRRGI
+IDKESGTYRNTLTGETMYVGDA
+>Gene.3::Ap7_1/1_1.000_421::g.3::m.3 Gene.3::Ap7_1/1_1.000_421::g.3  ORF type:internal len:141 (+) Ap7_1/1_1.000_421:1-420(+)
+FVMNLFDWYSAGYSIIIVAFFEVIAISWIYGLQRFKKDIQMMVGKGRWINASFYYYWYPT
+WFIISPALMLYILVTMSMQFAPITYGGSISYPSYADGIGFLMVGLALIYLPVLAMIEYCK
+AHGFFSTMQKILRPKPDWGP
+>Gene.36::Ap82_1/1_1.000_313::g.36::m.36 Gene.36::Ap82_1/1_1.000_313::g.36  ORF type:internal len:105 (+) Ap82_1/1_1.000_313:1-312(+)
+SLLREPASVCASSSRELAETCLRLLLKLDTTYTTTDEAITDLLTVTVCQLRLADGRLSQP
+TTTRPCSTDDVVYVPIPTEFFHSYSFEQLVAFYVQSAMTNQMPR
+>Gene.37::Ap85_1/1_1.000_386::g.37::m.37 Gene.37::Ap85_1/1_1.000_386::g.37  ORF type:internal len:129 (+) Ap85_1/1_1.000_386:1-384(+)
+SPAGRNVSWDRREAWYRDAERPRDYPPLPPPPPEVLRRSRSRSPIAPVAYSPRRSSPLRG
+HSPYQRGRSSPPPLPRGRTPPRGRTPPPPRGRTPPPRGHTPLQRGRSPLPHGRSPPRARS
+TPPLRATP
+>Gene.38::Ap87_1/1_1.000_309::g.38::m.38 Gene.38::Ap87_1/1_1.000_309::g.38  ORF type:internal len:104 (+) Ap87_1/1_1.000_309:1-309(+)
+EIPEILDMLPDYRGKRVLELGAGIGRFSGVLAKEAAHLTVVDFMESFVEKNKEINGHHTN
+IEFIQADVSKLEVPQKSFDLIFSNWLLMYMSDEELKTFFVNCL
+>Gene.39::Ap89_1/1_1.000_302::g.39::m.39 Gene.39::Ap89_1/1_1.000_302::g.39  ORF type:internal len:101 (+) Ap89_1/1_1.000_302:1-300(+)
+VYHIKAEREEQGNRFIYHIKTEREDITDDSSDIYDPPPIYVPVKVNSTSHTSPSSSTKIS
+IPFESPKGAKSPSAGTSWPKFTPDPERQPKLVLNPGKRRT
+>Gene.5::Ap8_1/1_1.000_417::g.5::m.5 Gene.5::Ap8_1/1_1.000_417::g.5  ORF type:internal len:140 (+) Ap8_1/1_1.000_417:1-417(+)
+AKTGFNTNNCYSTRFRNTFAYNQREWCSVLLCMTVLLLNMQRKRALPSSHLSINTAWYSG
+QGEQEERLIVSTRACSPTHTHTSSHVCTRTRRPKHTNTHTGSRMFIRHSSSSSCHSTRTT
+SRLSLGIIFLWANRGPIRQ
+>Gene.40::Ap90_1/1_1.000_351::g.40::m.40 Gene.40::Ap90_1/1_1.000_351::g.40  ORF type:internal len:118 (+) Ap90_1/1_1.000_351:1-351(+)
+DGALFGASGSSIRINGVDVVLASRLITRRVLPLSADLAVFASLFFYGMFSIFNHFVAVCF
+HGNMALILSRRNAADCLSAFMTFNFFILYDSAAYLQYFFVLLFFYLLFFLFISQLIV
+>Gene.6::Ap9_1/1_1.000_470::g.6::m.6 Gene.6::Ap9_1/1_1.000_470::g.6  ORF type:internal len:157 (+) Ap9_1/1_1.000_470:1-468(+)
+LEEEIEELMHENDDEDGVEVEKSKDKHESVERAEKRGSNKNDVKHDEKDRSKDNKENELG
+QIKEVEDMGPSVDRSENEREAVGKGIKSEQEGSGSKANKHQVSPTNQGCSHTTNESEKKE
+PSHPRSQSQQDSDDDDGEGETLHEKSSSEGDDEGNQ